Releases · mbari-org/annosaurus

03 Dec 19:22

hohonuuli

0.12.3

292f6f4

annosaurus 0.12.3

Code cleanup and Raziel integration

Full Changelog: 0.12.2...0.12.3

Assets 2

30 Nov 21:56

hohonuuli

0.12.2

bb5057a

annosaurus 0.12.2

This release upgrades Java from 11 to 17 (the latest long-term release)

There is a also a new endpoint for checking health of the server:

/health

Demo setup

docker run -p 8080:8080 -e BASICJWT_CLIENT_SECRET=foo -e BASICJWT_SIGNING_SECRET=bar mbari/annosaurus

Request

GET http://localhost:8080/v1/health

Response

HTTP/1.1 200 OK
Date: Tue, 30 Nov 2021 21:55:07 GMT
Content-Type: text/plain;charset=utf-8
Transfer-Encoding: chunked
Connection: close
Content-Encoding: gzip

{
  "jdkVersion": "17.0.1+12-39",
  "availableProcessors": 2,
  "freeMemory": 40227408,
  "maxMemory": 4294967296,
  "totalMemory": 94371840,
  "application": "annosaurus"
}

Full Changelog: 0.12.1...0.12.2

Assets 2

09 Nov 20:15

hohonuuli

0.12.1

fa1ed40

annosaurus 0.12.1

This release adds additional parameters to a query to constrain using missionContacts, missionId, and platformName. Some examples:

Search by platformName (e.g. ROV name) and a missionContact (e.g. A Chief Scientist)

In this query, we're searching for all annotations on dives by the ROV Doc Ricketts when Bruce Robison was the Chief Scientist. Because there's 1,019,079 annotations that match that query, we'll limit the number of returned annotations to 2 for this example.

Request

POST http://dsg.mbari.org/anno/v1/fast/
Content-Type: application/json

{
  "platformName": "Doc Ricketts",
  "missionContacts": ["Bruce Robison"],
  "limit": 2
}

Response

HTTP/1.1 200 OK
Server: nginx/1.20.1
Date: Tue, 09 Nov 2021 20:07:17 GMT
Content-Type: application/json;charset=utf-8
Transfer-Encoding: chunked
Connection: close
Access-Control-Allow-Origin: *
Content-Encoding: gzip

{
  "query_constraints": {
    "video_reference_uuids": [],
    "concepts": [],
    "observers": [],
    "groups": [],
    "activities": [],
    "limit": 2,
    "offset": 0,
    "data": false,
    "mission_contacts": [
      "Bruce Robison"
    ],
    "platform_name": "Doc Ricketts"
  },
  "content": [
    {
      "observation_uuid": "b8bec2c2-f755-4140-ff65-00000e76b81e",
      "concept": "Aegina",
      "observer": "mbassett",
      "observation_timestamp": "2021-03-17T20:39:30.920Z",
      "video_reference_uuid": "8e963a90-a7f0-49fc-8af6-1b0a23b2dd3a",
      "imaged_moment_uuid": "3fb36025-abe4-408a-a06c-18000e76b81e",
      "timecode": "09:56:04:27",
      "recorded_timestamp": "2013-11-12T00:42:59Z",
      "group": "ROV",
      "associations": [],
      "image_references": []
    },
    {
      "observation_uuid": "72c8cbba-4664-4296-a51f-0000285cb073",
      "concept": "Aegina",
      "observer": "svonthun",
      "observation_timestamp": "2014-02-10T20:09:00Z",
      "video_reference_uuid": "12948865-0f9e-4edc-8c88-db34746ea74e",
      "imaged_moment_uuid": "c6c36eb2-e833-4f9d-b4d4-60bd2c2ab5be",
      "timecode": "02:26:04:23",
      "recorded_timestamp": "2012-10-27T23:14:00Z",
      "group": "ROV",
      "associations": [],
      "image_references": []
    }
  ]
}

Search by missionId

A missionId is a unique id for the mission or deployment. (In VampireSquid, this is a deploymentId). In this query, we're searching for Ventana's 1234 dive.

Request

POST http://dsg.mbari.org/anno/v1/fast/
Content-Type: application/json

{
  "missionId": "Ventana 1234",
  "limit": "2"
}

Response

HTTP/1.1 200 OK
Server: nginx/1.20.1
Date: Tue, 09 Nov 2021 20:14:12 GMT
Content-Type: application/json;charset=utf-8
Transfer-Encoding: chunked
Connection: close
Access-Control-Allow-Origin: *
Content-Encoding: gzip

{
  "query_constraints": {
    "video_reference_uuids": [],
    "concepts": [],
    "observers": [],
    "groups": [],
    "activities": [],
    "limit": 2,
    "offset": 0,
    "data": false,
    "mission_contacts": [],
    "mission_id": "Ventana 1234"
  },
  "content": [
    {
      "observation_uuid": "fcbc98db-4ac0-4dd0-9ad8-014e5cc8811f",
      "concept": "Solmissus",
      "observer": "unknown",
      "observation_timestamp": "1970-01-01T00:00:00Z",
      "video_reference_uuid": "aefee7f8-53e1-4106-bcd0-e33f800e0bcb",
      "imaged_moment_uuid": "42ebf9cb-7d51-4262-9099-a926eea47a75",
      "timecode": "02:39:23:14",
      "recorded_timestamp": "1997-04-11T19:21:40Z",
      "group": "ROV",
      "associations": [
        {
          "link_name": "suspect-navigation-ctd-other-data",
          "link_value": "No CTD data",
          "to_concept": "self",
          "mime_type": "text/plain",
          "uuid": "389672bc-b023-4ca0-9c52-3d4211d9280d"
        }
      ],
      "image_references": []
    },
    {
      "observation_uuid": "06515cd5-21d4-445b-8958-02a165dc018f",
      "concept": "Nanomia bijuga",
      "observer": "unknown",
      "observation_timestamp": "1970-01-01T00:00:00Z",
      "video_reference_uuid": "aefee7f8-53e1-4106-bcd0-e33f800e0bcb",
      "imaged_moment_uuid": "545a814f-141b-4b1e-9a9e-18f386ec2389",
      "timecode": "02:39:16:12",
      "recorded_timestamp": "1997-04-11T19:21:31Z",
      "group": "ROV",
      "associations": [
        {
          "link_name": "suspect-navigation-ctd-other-data",
          "link_value": "No CTD data",
          "to_concept": "self",
          "mime_type": "text/plain",
          "uuid": "3932da8c-2358-4754-8a30-3301c0cc6346"
        }
      ],
      "image_references": []
    }
  ]
}

Assets 2

29 Jun 17:42

hohonuuli

0.11.1

ba5d782

annosaurus 0.11.1

This is a minor bug fix release. It addresses an issue where an observation without an observation_timestamp would cause calls to "fast" endpoints to fail.

Assets 2

14 Apr 23:23

hohonuuli

0.11.0

a42b875

annosaurus 0.11.0

MBARI is revamping our Deep-sea Guide. In order to support it, we're adding some basic analysis endpoints to annosaurus. This release allows add hoc queries to generate data histograms. Here's an example to get a frequency histogram for annotations with the matching concepts and observer. (Note that ?size=50 sets the vertical depth bin size to 50 meters)

Request

POST http://dsg.mbari.org/anno/v1/analysis/histogram/depth?size=50
Content-Type: application/json

{
  concepts: ["Nanomia", "Nanomia bijuga"],
  observers: ["schlin"]
}

Response

HTTP/1.1 200 OK
Server: nginx/1.16.1
Date: Wed, 14 Apr 2021 23:21:31 GMT
Content-Type: application/json;charset=utf-8
Transfer-Encoding: chunked
Connection: close
Access-Control-Allow-Origin: *
Content-Encoding: gzip

{
  "query_constraints": {
    "video_reference_uuids": [],
    "concepts": [
      "Nanomia",
      "Nanomia bijuga"
    ],
    "observers": [
      "schlin"
    ],
    "groups": [],
    "activities": [],
    "limit": 5000,
    "offset": 0,
    "data": false
  },
  "content": {
    "bins_min": [
      0,
      50,
      100,
      150,
      200,
      250,
      300,
      350,
      400,
      450,
      500,
      550,
      600,
      650,
      700,
      750,
      800,
      850,
      900,
      950,
      1000,
      1050,
      1100,
      1150,
      1200,
      1250,
      1300,
      1350,
      1400,
      1450,
      1500,
      1550,
      1600,
      1650,
      1700,
      1750,
      1800,
      1850,
      1900,
      1950,
      2000,
      2050,
      2100,
      2150,
      2200,
      2250,
      2300,
      2350,
      2400,
      2450,
      2500,
      2550,
      2600,
      2650,
      2700,
      2750,
      2800,
      2850,
      2900,
      2950,
      3000,
      3050,
      3100,
      3150,
      3200,
      3250,
      3300,
      3350,
      3400,
      3450,
      3500,
      3550,
      3600,
      3650,
      3700,
      3750,
      3800,
      3850,
      3900,
      3950
    ],
    "bins_max": [
      50,
      100,
      150,
      200,
      250,
      300,
      350,
      400,
      450,
      500,
      550,
      600,
      650,
      700,
      750,
      800,
      850,
      900,
      950,
      1000,
      1050,
      1100,
      1150,
      1200,
      1250,
      1300,
      1350,
      1400,
      1450,
      1500,
      1550,
      1600,
      1650,
      1700,
      1750,
      1800,
      1850,
      1900,
      1950,
      2000,
      2050,
      2100,
      2150,
      2200,
      2250,
      2300,
      2350,
      2400,
      2450,
      2500,
      2550,
      2600,
      2650,
      2700,
      2750,
      2800,
      2850,
      2900,
      2950,
      3000,
      3050,
      3100,
      3150,
      3200,
      3250,
      3300,
      3350,
      3400,
      3450,
      3500,
      3550,
      3600,
      3650,
      3700,
      3750,
      3800,
      3850,
      3900,
      3950,
      4000
    ],
    "values": [
      3313,
      3755,
      3953,
      5136,
      7181,
      7772,
      8253,
      6784,
      6304,
      5741,
      2626,
      1341,
      816,
      278,
      66,
      9,
      6,
      28,
      4,
      16,
      25,
      2,
      4,
      1,
      68,
      0,
      0,
      2,
      0,
      0,
      0,
      4,
      1,
      2,
      1,
      0,
      0,
      0,
      1,
      5,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0,
      0
    ]
  }
}

Assets 2

09 Apr 17:34

hohonuuli

0.10.0

88aa8a7

annosaurus 0.10.0

This release adds a query to look up the geographic range of observations. It returns the max latitude, longitude and depth extents for annotations that match the query constraints provided. For example:

Request

POST http://dsg.mbari.org/anno/v1/fast/georange
Content-Type: application/json

{
  concepts: ["Pandalus", "Pandalus platyceros"]
}

Response

HTTP/1.1 200 OK
Server: nginx/1.16.1
Date: Fri, 09 Apr 2021 17:32:18 GMT
Content-Type: application/json;charset=utf-8
Transfer-Encoding: chunked
Connection: close
Access-Control-Allow-Origin: *
Content-Encoding: gzip

{
  "query_constraints": {
    "video_reference_uuids": [],
    "concepts": [
      "Pandalus",
      "Pandalus platyceros"
    ],
    "observers": [],
    "groups": [],
    "activities": [],
    "limit": 5000,
    "offset": 0,
    "data": false
  },
  "content": {
    "min_latitude": 0.0,
    "max_latitude": 40.4352,
    "min_longitude": -126.414553,
    "max_longitude": 0.0,
    "min_depth_meters": 59.1,
    "max_depth_meters": 2648.38
  }
}

Assets 2

08 Mar 18:04

hohonuuli

0.9.2

365c9b4

annosaurus 0.9.2

I've added a new endpoint (as requested by CSIRO) for retrieving imagedMoments that have at least one image (i.e. ImageReference) and that have an Association that matches the user-provided toConcept. The endpoint is:

http://my.annosaurus.org/anno/v1/fast/imagedmoments/toconcept/images/{to_concept}

It returns a list of ImagedMoment UUIDS:

[
  "9c1cef8a-aed6-469d-accb-04c3aa82e3b1",
  "70f807b7-1cdd-4023-8c32-0ee3d80a4f32",
  "43e02cd8-41dd-4b97-a437-0f34a9cb3daf",
  "c8d54faa-91be-410a-9d2a-1c6ea2b8fa90",
  "ee26d184-4759-4fe4-a47f-3a621878fdc5"
]

This release also includes a bug fix for a rare NullPointerException that could occur if an association was missing a linkValue.

Assets 2

07 Jan 02:09

hohonuuli

0.8.0

5c5fe17

annosaurus 0.8.0

Added new endpoints for flexible queries:

POST /anno/v1/fast/ - Retrieve annotations
POST /anno/v1/fast/count - Retrieve a count of the annotations that match the query

Both of these accept a json body that defines various constraints. Any of these constraints can be omitted. Full examples are:

camelCase

{
  "videoReferenceUuids": [
      "43c8e033-eb22-4905-b39b-0a3e66a0075b"
  ],
  "concepts": [
    "Aegina",
    "Aegina citrea"
  ],
  "groups": [
      "ROV"
  ],
  "activities": [
      "descent",
      "transect"
  ],
  "observers": [
      "kwalz"
  ],
  "minDepth": 200,
  "maxDepth": 300,
  "minLatitude": 35.0,
  "maxLatitude": 37.0,
  "minLongitude": -122.7,
  "maxLongitude": -122.0,
  "minTimestamp": "1998-01-01T00:00:00Z",
  "maxTimestamp": "2021-01-07T00:53:32.757470Z",
  "linkName": "eating",
  "linkValue": "nil",
  "limit": 5000,
  "offset": 0,
  "data": true
}

snake_case

{
  "video_reference_uuids": [
      "43c8e033-eb22-4905-b39b-0a3e66a0075b"
  ],
  "concepts": [
    "Aegina",
    "Aegina citrea"
  ],
  "groups": [
      "ROV"
  ],
  "activities": [
      "descent",
      "transect"
  ],
  "observers": [
      "kwalz"
  ],
  "min_depth": 200,
  "max_depth": 300,
  "min_latitude": 35.0,
  "max_latitude": 37.0,
  "min_longitude": -122.7,
  "max_longitude": -122.0,
  "min_timestamp": "1998-01-01T00:00:00Z",
  "max_timestamp": "2021-01-07T00:53:32.757470Z",
  "link_name": "eating",
  "link_value": "nil",
  "limit": 5000,
  "offset": 0,
  "data": true
}

The response will be JSON in the form like:

{
    "query_constraints": {
        "video_reference_uuids": [
            "43c8e033-eb22-4905-b39b-0a3e66a0075b"
        ],
        "concepts": [
            "Aegina",
            "Aegina citrea"
        ],
        "observers": [
            "kwalz"
        ],
        "groups": [
            "ROV"
        ],
        "activities": [
            "descent",
            "transect"
        ],
        "min_depth": 200.0,
        "max_depth": 300.0,
        "min_timestamp": "1998-01-01T00:00:00Z",
        "max_timestamp": "2021-01-07T00:53:32.757470Z",
        "link_name": "eating",
        "link_value": "nil",
        "limit": 5000,
        "offset": 0,
        "data": true
    },
    "content": [
        {
            "ancillary_data": {
                "oxygen_ml_l": 1.125,
                "depth_meters": 299.3599853515625,
                "latitude": 36.701864,
                "temperature_celsius": 8.234999656677246,
                "theta": 3.799999952316284,
                "longitude": -122.050932,
                "phi": -3.299999952316284,
                "psi": 235.0,
                "pressure_dbar": 303.1000061035156,
                "salinity": 34.1609992980957,
                "altitude": 78.11000061035156,
                "light_transmission": 79.2699966430664,
                "uuid": "c34c0113-3aaa-4648-a704-3472f3f0f42d"
            },
            "observation_uuid": "5281db41-5914-4929-a298-48de0d26782d",
            "concept": "Physonectae",
            "observer": "kwalz",
            "observation_timestamp": "2013-11-25T19:52:38.957Z",
            "video_reference_uuid": "43c8e033-eb22-4905-b39b-0a3e66a0075b",
            "imaged_moment_uuid": "ab905fde-a8a1-4f23-b4bd-d28bf92a062e",
            "timecode": "00:45:56:04",
            "recorded_timestamp": "2013-11-08T15:11:58Z",
            "group": "ROV",
            "activity": "transect",
            "associations": [
                {
                    "link_name": "eating",
                    "link_value": "nil",
                    "to_concept": "Aegina",
                    "mime_type": "text/plain",
                    "uuid": "07a76fdb-11ff-437b-b2e4-4f7e312e806a"
                },
                {
                    "link_name": "comment",
                    "link_value": "wuzzle?",
                    "to_concept": "self",
                    "mime_type": "text/plain",
                    "uuid": "99fb539a-4578-46d2-aa8c-8a43e40e168f"
                }
            ],
            "image_references": []
        }
    ]
}

Here's a an example using curl:

curl --header "Content-type: application/json" \
    --request POST \
    --data '{"concepts": ["Aegina", "Aegina citrea"], "link_name": "eating", "limit": 5000, "offset": 0, "data": true}' \
    http://m3.shore.mbari.org/anno/v1/fast/

Notes

SQL expansion

Under the hood, concepts: ["Aegina", "Aegina citrea"] is expanded to the SQL (observation.concept IN ('Aegina', 'Aegina citrea') OR association.to_concept IN ('Aegina', 'Aegina citrea')

{concept: ["Aegina"], link_name: "eating"} is expanded to the SQL:

(
  observation.concept IN ('Aegina') OR 
  association.to_concept IN  ('Aegina')
) 
AND association.link_name = "eating"

Min params like minDepth are inclusive and so become AND ancillary_data.depth_meters >= minDepth in SQL. Max params are exclusive, i.e. maxDepth becomes AND ancillary_data.depth_meters < maxDepth

Assets 2

12 Jun 21:58

hohonuuli

0.7.0

fc9c32c

annosaurus 0.7.0

The following changes were added:

Upgrade to scala 2.13 and Scalatra 2.7.0.
Added colorized logging
Added anno/v1/observations/delete/duration/{:uuid} endpoint.

Assets 2

05 Mar 00:54

hohonuuli

0.6.3

8fe9887

annosaurus 0.6.3

Added support for message publishing when an Association is created or updated. ZeroMq subscribers will see a message like:

{
  "observation_uuid": "e7bcf8d6-880e-4ead-3763-7b3185e7a51e",
  "link_name": "eating",
  "to_concept": "Pandalus platyceros",
  "link_value": "nil",
  "mime_type": "text/plain",
  "object_type": "Association"
}

Assets 2

Provide feedback

Saved searches

Use saved searches to filter your results more quickly

/health

Demo setup

Request

Response

Search by platformName (e.g. ROV name) and a missionContact (e.g. A Chief Scientist)

Request

Response

Search by missionId

Request

Response

Request

Response

Notes

SQL expansion

Releases: mbari-org/annosaurus

annosaurus 0.12.3

annosaurus 0.12.2

/health

Demo setup

Request

Response

annosaurus 0.12.1

Search by platformName (e.g. ROV name) and a missionContact (e.g. A Chief Scientist)

Request

Response

Search by missionId

Request

Response

annosaurus 0.11.1

annosaurus 0.11.0

annosaurus 0.10.0

Request

Response

annosaurus 0.9.2

annosaurus 0.8.0

Notes

SQL expansion

annosaurus 0.7.0

annosaurus 0.6.3